Starting phenix.real_space_refine on Sat Jul 26 12:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jvp_22509/07_2025/7jvp_22509.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvp_22509/07_2025/7jvp_22509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2025/7jvp_22509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2025/7jvp_22509.map" model { file = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2025/7jvp_22509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2025/7jvp_22509.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 5462 2.51 5 N 1440 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2227 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 3 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1966 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2604 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 280 Unusual residues: {'CLR': 6, 'PLM': 5, 'SK9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 5.57, per 1000 atoms: 0.66 Number of scatterers: 8486 At special positions: 0 Unit cell: (97.185, 106.59, 122.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 53 16.00 O 1530 8.00 N 1440 7.00 C 5462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 45.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 51 through 57 removed outlier: 3.519A pdb=" N ARG R 55 " --> pdb=" O PHE R 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 4.392A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.661A pdb=" N LYS R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.380A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.141A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 239 Processing helix chain 'R' and resid 265 through 299 Proline residue: R 287 - end of helix Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 332 removed outlier: 3.598A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.877A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.244A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.671A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 312 through 317 removed outlier: 4.033A pdb=" N ALA A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 317' Processing helix chain 'A' and resid 331 through 353 Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.504A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.924A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.744A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.880A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.182A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.704A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.864A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.855A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.051A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2656 1.34 - 1.46: 1951 1.46 - 1.58: 3987 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8667 Sorted by residual: bond pdb=" N LEU R 291 " pdb=" CA LEU R 291 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.36e+00 bond pdb=" N PHE R 313 " pdb=" CA PHE R 313 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.74e+00 bond pdb=" C05 SK9 R 501 " pdb=" C07 SK9 R 501 " ideal model delta sigma weight residual 1.520 1.561 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C ILE R 205 " pdb=" N PRO R 206 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.11e+00 bond pdb=" C18 SK9 R 501 " pdb=" N01 SK9 R 501 " ideal model delta sigma weight residual 1.448 1.409 0.039 2.00e-02 2.50e+03 3.83e+00 ... (remaining 8662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11122 2.01 - 4.01: 535 4.01 - 6.02: 63 6.02 - 8.03: 18 8.03 - 10.03: 3 Bond angle restraints: 11741 Sorted by residual: angle pdb=" C CYS A 365 " pdb=" N SER A 366 " pdb=" CA SER A 366 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" N LEU R 295 " pdb=" CA LEU R 295 " pdb=" C LEU R 295 " ideal model delta sigma weight residual 113.16 118.65 -5.49 1.42e+00 4.96e-01 1.49e+01 angle pdb=" C CYS B 250 " pdb=" N ARG B 251 " pdb=" CA ARG B 251 " ideal model delta sigma weight residual 122.99 117.69 5.30 1.41e+00 5.03e-01 1.41e+01 angle pdb=" C CYS B 166 " pdb=" N ALA B 167 " pdb=" CA ALA B 167 " ideal model delta sigma weight residual 122.62 117.27 5.35 1.56e+00 4.11e-01 1.18e+01 angle pdb=" C07 SK9 R 501 " pdb=" C09 SK9 R 501 " pdb=" N01 SK9 R 501 " ideal model delta sigma weight residual 114.07 124.10 -10.03 3.00e+00 1.11e-01 1.12e+01 ... (remaining 11736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 5207 15.07 - 30.14: 224 30.14 - 45.22: 35 45.22 - 60.29: 9 60.29 - 75.36: 2 Dihedral angle restraints: 5477 sinusoidal: 2448 harmonic: 3029 Sorted by residual: dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual -86.00 -115.08 29.08 1 1.00e+01 1.00e-02 1.21e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1133 0.087 - 0.174: 163 0.174 - 0.261: 22 0.261 - 0.348: 6 0.348 - 0.435: 6 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 1327 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 380 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG A 380 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 380 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 381 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 375 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C VAL A 375 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 375 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 376 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.049 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO A 361 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.041 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 474 2.75 - 3.28: 8315 3.28 - 3.82: 14214 3.82 - 4.36: 16907 4.36 - 4.90: 29451 Nonbonded interactions: 69361 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.254 3.040 nonbonded pdb=" O SER R 198 " pdb=" OG SER R 202 " model vdw 2.264 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.268 3.040 ... (remaining 69356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.450 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8670 Z= 0.260 Angle : 0.966 10.032 11747 Z= 0.535 Chirality : 0.070 0.435 1330 Planarity : 0.007 0.075 1447 Dihedral : 9.005 75.358 3500 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.24), residues: 1021 helix: 3.52 (0.21), residues: 423 sheet: 2.92 (0.34), residues: 196 loop : -1.16 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 281 HIS 0.019 0.004 HIS A 220 PHE 0.041 0.004 PHE B 234 TYR 0.023 0.003 TYR A 311 ARG 0.018 0.001 ARG R 266 Details of bonding type rmsd hydrogen bonds : bond 0.13726 ( 462) hydrogen bonds : angle 6.22628 ( 1347) SS BOND : bond 0.00381 ( 3) SS BOND : angle 1.97513 ( 6) covalent geometry : bond 0.00503 ( 8667) covalent geometry : angle 0.96507 (11741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 278 MET cc_start: 0.7523 (mmm) cc_final: 0.7254 (mmp) REVERT: A 17 LYS cc_start: 0.7640 (tttt) cc_final: 0.7074 (mmmt) REVERT: A 378 ASP cc_start: 0.7661 (m-30) cc_final: 0.7406 (m-30) REVERT: B 161 SER cc_start: 0.8590 (t) cc_final: 0.8083 (m) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 1.1168 time to fit residues: 294.2443 Evaluate side-chains 149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 53 HIS ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 294 GLN A 384 GLN B 6 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 110 ASN B 156 GLN B 259 GLN N 31 ASN N 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.161037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128649 restraints weight = 9804.282| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.79 r_work: 0.3294 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8670 Z= 0.166 Angle : 0.562 7.489 11747 Z= 0.303 Chirality : 0.043 0.154 1330 Planarity : 0.005 0.057 1447 Dihedral : 6.574 57.283 1608 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.91 % Allowed : 11.76 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.25), residues: 1021 helix: 3.19 (0.23), residues: 423 sheet: 1.79 (0.33), residues: 210 loop : -0.58 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 281 HIS 0.011 0.002 HIS A 357 PHE 0.017 0.002 PHE R 288 TYR 0.014 0.002 TYR B 59 ARG 0.009 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 462) hydrogen bonds : angle 4.82275 ( 1347) SS BOND : bond 0.00715 ( 3) SS BOND : angle 1.11667 ( 6) covalent geometry : bond 0.00362 ( 8667) covalent geometry : angle 0.56207 (11741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 1.015 Fit side-chains REVERT: R 50 ARG cc_start: 0.6639 (mmt90) cc_final: 0.5674 (tpp-160) REVERT: R 59 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8661 (p) REVERT: R 213 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8537 (m) REVERT: R 216 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7775 (mtt180) REVERT: R 219 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7483 (mtt-85) REVERT: R 278 MET cc_start: 0.8147 (mmm) cc_final: 0.7856 (mmp) REVERT: A 17 LYS cc_start: 0.7357 (tttt) cc_final: 0.6583 (mmmt) REVERT: A 344 GLU cc_start: 0.7903 (tp30) cc_final: 0.7671 (tp30) REVERT: A 378 ASP cc_start: 0.8336 (m-30) cc_final: 0.8098 (m-30) REVERT: A 386 MET cc_start: 0.8899 (ttm) cc_final: 0.8598 (ttp) REVERT: B 96 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7856 (mtp85) REVERT: B 266 HIS cc_start: 0.7854 (t-170) cc_final: 0.7618 (t-170) REVERT: B 325 MET cc_start: 0.8772 (tpp) cc_final: 0.8563 (tpp) REVERT: N 5 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7118 (tm-30) REVERT: N 46 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8114 (pm20) outliers start: 26 outliers final: 7 residues processed: 199 average time/residue: 1.2934 time to fit residues: 273.0933 Evaluate side-chains 159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 65 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 259 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125257 restraints weight = 9703.572| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.87 r_work: 0.3214 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8670 Z= 0.158 Angle : 0.531 7.866 11747 Z= 0.284 Chirality : 0.041 0.136 1330 Planarity : 0.004 0.038 1447 Dihedral : 6.435 57.667 1608 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.26 % Allowed : 15.01 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1021 helix: 2.82 (0.24), residues: 429 sheet: 1.00 (0.31), residues: 210 loop : -0.37 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.009 0.001 HIS A 357 PHE 0.025 0.002 PHE R 297 TYR 0.012 0.002 TYR A 339 ARG 0.006 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 462) hydrogen bonds : angle 4.72695 ( 1347) SS BOND : bond 0.01876 ( 3) SS BOND : angle 1.39768 ( 6) covalent geometry : bond 0.00345 ( 8667) covalent geometry : angle 0.53018 (11741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.933 Fit side-chains REVERT: R 50 ARG cc_start: 0.6719 (mmt90) cc_final: 0.5732 (tpp-160) REVERT: R 59 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8728 (p) REVERT: R 213 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8710 (m) REVERT: R 219 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7387 (mtt-85) REVERT: R 278 MET cc_start: 0.8315 (mmm) cc_final: 0.8064 (mmp) REVERT: A 17 LYS cc_start: 0.7274 (tttt) cc_final: 0.6480 (mmmt) REVERT: A 27 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 265 ARG cc_start: 0.7740 (ptt180) cc_final: 0.7382 (ppt-90) REVERT: A 307 LYS cc_start: 0.4888 (mmtt) cc_final: 0.4659 (mtpm) REVERT: A 330 GLU cc_start: 0.5934 (tt0) cc_final: 0.5160 (tp30) REVERT: A 344 GLU cc_start: 0.7986 (tp30) cc_final: 0.7767 (tp30) REVERT: A 370 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6970 (pt0) REVERT: A 386 MET cc_start: 0.8944 (ttm) cc_final: 0.8642 (ttp) REVERT: B 42 ARG cc_start: 0.6971 (tpt170) cc_final: 0.6742 (tpt170) REVERT: B 96 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7886 (mtp85) REVERT: B 262 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8225 (ttm) REVERT: B 325 MET cc_start: 0.8778 (tpp) cc_final: 0.8543 (tpp) REVERT: G 46 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7462 (mppt) REVERT: N 5 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7047 (tm-30) REVERT: N 38 ARG cc_start: 0.8669 (ptt-90) cc_final: 0.8253 (ptp90) REVERT: N 46 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8151 (pm20) outliers start: 38 outliers final: 17 residues processed: 169 average time/residue: 1.2790 time to fit residues: 230.1437 Evaluate side-chains 156 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 259 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113020 restraints weight = 9674.863| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.00 r_work: 0.3135 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8670 Z= 0.176 Angle : 0.536 7.757 11747 Z= 0.285 Chirality : 0.042 0.137 1330 Planarity : 0.004 0.044 1447 Dihedral : 6.333 55.338 1608 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.70 % Allowed : 15.23 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1021 helix: 2.52 (0.24), residues: 430 sheet: 0.38 (0.31), residues: 216 loop : -0.22 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 281 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 288 TYR 0.013 0.002 TYR R 194 ARG 0.009 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 462) hydrogen bonds : angle 4.87211 ( 1347) SS BOND : bond 0.00406 ( 3) SS BOND : angle 1.23780 ( 6) covalent geometry : bond 0.00395 ( 8667) covalent geometry : angle 0.53571 (11741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.887 Fit side-chains REVERT: R 50 ARG cc_start: 0.6826 (mmt90) cc_final: 0.5891 (tpp-160) REVERT: R 154 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7921 (tt) REVERT: R 213 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8532 (p) REVERT: R 219 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7558 (mtt-85) REVERT: R 223 LYS cc_start: 0.8037 (mttt) cc_final: 0.7837 (mtpt) REVERT: R 265 LYS cc_start: 0.7620 (tttt) cc_final: 0.7306 (tmtm) REVERT: R 278 MET cc_start: 0.8670 (mmm) cc_final: 0.8355 (mmp) REVERT: A 17 LYS cc_start: 0.7370 (tttt) cc_final: 0.6630 (mmmt) REVERT: A 265 ARG cc_start: 0.7847 (ptt180) cc_final: 0.7532 (ppt-90) REVERT: A 370 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: A 378 ASP cc_start: 0.8636 (m-30) cc_final: 0.8114 (m-30) REVERT: A 386 MET cc_start: 0.9015 (ttm) cc_final: 0.8756 (ttp) REVERT: B 42 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6904 (tpt170) REVERT: B 96 ARG cc_start: 0.8311 (mtt180) cc_final: 0.8025 (mtp85) REVERT: G 46 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7485 (mppt) REVERT: N 3 GLN cc_start: 0.8197 (pt0) cc_final: 0.7306 (tp-100) REVERT: N 5 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7138 (tm-30) REVERT: N 38 ARG cc_start: 0.8789 (ptt-90) cc_final: 0.8380 (ptp90) REVERT: N 46 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8275 (pm20) outliers start: 42 outliers final: 19 residues processed: 178 average time/residue: 1.2754 time to fit residues: 240.6749 Evaluate side-chains 159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 259 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.149192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113717 restraints weight = 9631.036| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.97 r_work: 0.3133 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8670 Z= 0.149 Angle : 0.507 6.752 11747 Z= 0.271 Chirality : 0.040 0.137 1330 Planarity : 0.004 0.039 1447 Dihedral : 6.248 56.870 1608 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.04 % Allowed : 16.46 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1021 helix: 2.65 (0.24), residues: 425 sheet: 0.23 (0.31), residues: 216 loop : -0.21 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 99 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.001 PHE R 288 TYR 0.015 0.001 TYR N 95 ARG 0.009 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 462) hydrogen bonds : angle 4.80936 ( 1347) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.92369 ( 6) covalent geometry : bond 0.00328 ( 8667) covalent geometry : angle 0.50714 (11741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.882 Fit side-chains REVERT: R 50 ARG cc_start: 0.6815 (mmt90) cc_final: 0.5896 (tpm170) REVERT: R 57 LYS cc_start: 0.7180 (mttt) cc_final: 0.6800 (mtmm) REVERT: R 213 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8438 (p) REVERT: R 219 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7534 (mtt-85) REVERT: R 265 LYS cc_start: 0.7590 (tttt) cc_final: 0.7296 (tmtm) REVERT: A 17 LYS cc_start: 0.7369 (tttt) cc_final: 0.6651 (mmmt) REVERT: A 265 ARG cc_start: 0.7856 (ptt180) cc_final: 0.7543 (ppt-90) REVERT: A 314 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: A 356 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7606 (tpp80) REVERT: A 370 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: A 378 ASP cc_start: 0.8627 (m-30) cc_final: 0.8161 (m-30) REVERT: A 386 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8725 (ttp) REVERT: B 42 ARG cc_start: 0.7120 (tpt170) cc_final: 0.6906 (tpt170) REVERT: G 46 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7480 (mppt) REVERT: N 3 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: N 5 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7496 (tm-30) REVERT: N 38 ARG cc_start: 0.8767 (ptt-90) cc_final: 0.8439 (ptp90) REVERT: N 46 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: N 87 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7949 (mtmt) outliers start: 45 outliers final: 18 residues processed: 167 average time/residue: 1.3486 time to fit residues: 238.0277 Evaluate side-chains 151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 97 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119176 restraints weight = 9614.950| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.96 r_work: 0.3217 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8670 Z= 0.109 Angle : 0.474 6.168 11747 Z= 0.253 Chirality : 0.039 0.136 1330 Planarity : 0.004 0.037 1447 Dihedral : 5.873 58.061 1608 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.26 % Allowed : 18.03 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1021 helix: 2.74 (0.24), residues: 431 sheet: 0.19 (0.32), residues: 208 loop : -0.19 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 288 TYR 0.016 0.001 TYR N 95 ARG 0.007 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 462) hydrogen bonds : angle 4.61799 ( 1347) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.84038 ( 6) covalent geometry : bond 0.00226 ( 8667) covalent geometry : angle 0.47347 (11741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.896 Fit side-chains REVERT: R 50 ARG cc_start: 0.6663 (mmt90) cc_final: 0.5682 (tpp-160) REVERT: R 57 LYS cc_start: 0.7238 (mttt) cc_final: 0.6921 (mtmm) REVERT: R 213 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8655 (m) REVERT: R 219 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7490 (mtt-85) REVERT: R 265 LYS cc_start: 0.7581 (tttt) cc_final: 0.7276 (tmtm) REVERT: R 278 MET cc_start: 0.8554 (mmm) cc_final: 0.8220 (mmp) REVERT: A 17 LYS cc_start: 0.7432 (tttt) cc_final: 0.6669 (mmmt) REVERT: A 265 ARG cc_start: 0.7826 (ptt180) cc_final: 0.7602 (ppt-90) REVERT: A 299 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: A 314 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: A 356 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7508 (tpp80) REVERT: A 378 ASP cc_start: 0.8572 (m-30) cc_final: 0.8130 (m-30) REVERT: A 386 MET cc_start: 0.8992 (ttm) cc_final: 0.8715 (ttp) REVERT: N 3 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: N 5 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7128 (tm-30) REVERT: N 38 ARG cc_start: 0.8683 (ptt-90) cc_final: 0.8418 (ptp90) REVERT: N 87 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7894 (mtmt) REVERT: N 109 ASP cc_start: 0.7261 (m-30) cc_final: 0.7034 (m-30) REVERT: N 110 VAL cc_start: 0.9005 (t) cc_final: 0.8663 (m) outliers start: 38 outliers final: 22 residues processed: 167 average time/residue: 1.2111 time to fit residues: 215.1236 Evaluate side-chains 153 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 259 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.151653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116557 restraints weight = 9753.937| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.00 r_work: 0.3194 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8670 Z= 0.123 Angle : 0.489 5.848 11747 Z= 0.260 Chirality : 0.039 0.135 1330 Planarity : 0.004 0.037 1447 Dihedral : 5.836 57.018 1608 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.25 % Allowed : 19.37 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1021 helix: 2.71 (0.24), residues: 432 sheet: 0.15 (0.32), residues: 206 loop : -0.20 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 362 PHE 0.017 0.001 PHE R 288 TYR 0.014 0.001 TYR N 95 ARG 0.007 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 462) hydrogen bonds : angle 4.63311 ( 1347) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.87940 ( 6) covalent geometry : bond 0.00266 ( 8667) covalent geometry : angle 0.48838 (11741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.883 Fit side-chains REVERT: R 50 ARG cc_start: 0.6591 (mmt90) cc_final: 0.5666 (tpp-160) REVERT: R 57 LYS cc_start: 0.7258 (mttt) cc_final: 0.6917 (mtmm) REVERT: R 213 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8667 (m) REVERT: R 219 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7510 (mtt-85) REVERT: R 265 LYS cc_start: 0.7544 (tttt) cc_final: 0.7231 (tmtm) REVERT: A 17 LYS cc_start: 0.7453 (tttt) cc_final: 0.6666 (mmmt) REVERT: A 265 ARG cc_start: 0.7861 (ptt180) cc_final: 0.7636 (ppt-90) REVERT: A 299 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: A 314 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: A 356 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7506 (tpp80) REVERT: A 370 GLU cc_start: 0.7684 (pm20) cc_final: 0.6991 (mm-30) REVERT: A 386 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8723 (ttp) REVERT: N 3 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: N 5 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7161 (tm-30) REVERT: N 38 ARG cc_start: 0.8600 (ptt-90) cc_final: 0.8210 (ptp90) REVERT: N 82 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8418 (tp40) REVERT: N 87 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7914 (mtmt) REVERT: N 110 VAL cc_start: 0.9032 (t) cc_final: 0.8664 (m) outliers start: 29 outliers final: 19 residues processed: 157 average time/residue: 1.3396 time to fit residues: 222.6986 Evaluate side-chains 156 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.153981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120125 restraints weight = 9876.241| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.91 r_work: 0.3186 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8670 Z= 0.119 Angle : 0.492 9.285 11747 Z= 0.260 Chirality : 0.039 0.134 1330 Planarity : 0.004 0.037 1447 Dihedral : 5.773 59.587 1608 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.81 % Allowed : 19.82 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1021 helix: 2.69 (0.24), residues: 432 sheet: 0.02 (0.32), residues: 213 loop : -0.15 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS A 362 PHE 0.017 0.001 PHE R 288 TYR 0.012 0.001 TYR N 95 ARG 0.007 0.000 ARG R 226 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 462) hydrogen bonds : angle 4.60641 ( 1347) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.85653 ( 6) covalent geometry : bond 0.00257 ( 8667) covalent geometry : angle 0.49192 (11741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.896 Fit side-chains REVERT: R 50 ARG cc_start: 0.6595 (mmt90) cc_final: 0.5749 (tpm170) REVERT: R 57 LYS cc_start: 0.7304 (mttt) cc_final: 0.6963 (mtmm) REVERT: R 59 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8747 (t) REVERT: R 213 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8633 (m) REVERT: R 219 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7472 (mtt-85) REVERT: R 265 LYS cc_start: 0.7550 (tttt) cc_final: 0.7215 (tmtm) REVERT: A 17 LYS cc_start: 0.7389 (tttt) cc_final: 0.6596 (mmmt) REVERT: A 265 ARG cc_start: 0.7855 (ptt180) cc_final: 0.7632 (ppt-90) REVERT: A 299 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: A 314 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: A 356 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7487 (tpp80) REVERT: A 378 ASP cc_start: 0.8599 (m-30) cc_final: 0.8144 (m-30) REVERT: B 124 TYR cc_start: 0.8906 (m-80) cc_final: 0.8489 (m-80) REVERT: N 3 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: N 5 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7129 (tm-30) REVERT: N 87 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7903 (mtmt) REVERT: N 110 VAL cc_start: 0.9001 (t) cc_final: 0.8659 (m) outliers start: 34 outliers final: 22 residues processed: 155 average time/residue: 1.3121 time to fit residues: 215.7652 Evaluate side-chains 155 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115174 restraints weight = 9770.187| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.91 r_work: 0.3142 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8670 Z= 0.151 Angle : 0.515 8.669 11747 Z= 0.273 Chirality : 0.040 0.135 1330 Planarity : 0.004 0.042 1447 Dihedral : 5.965 58.033 1608 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.70 % Allowed : 20.27 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1021 helix: 2.47 (0.24), residues: 438 sheet: -0.06 (0.32), residues: 218 loop : -0.18 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.001 PHE R 288 TYR 0.011 0.001 TYR N 95 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 462) hydrogen bonds : angle 4.75127 ( 1347) SS BOND : bond 0.00072 ( 3) SS BOND : angle 1.11721 ( 6) covalent geometry : bond 0.00337 ( 8667) covalent geometry : angle 0.51467 (11741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.912 Fit side-chains REVERT: R 50 ARG cc_start: 0.6664 (mmt90) cc_final: 0.5832 (tpm170) REVERT: R 57 LYS cc_start: 0.7346 (mttt) cc_final: 0.6979 (mtmm) REVERT: R 92 PHE cc_start: 0.4087 (m-80) cc_final: 0.3389 (m-80) REVERT: R 213 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8651 (m) REVERT: R 219 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7502 (mtt-85) REVERT: R 265 LYS cc_start: 0.7557 (tttt) cc_final: 0.7217 (tmtm) REVERT: R 278 MET cc_start: 0.8655 (mmm) cc_final: 0.8390 (mmm) REVERT: A 17 LYS cc_start: 0.7412 (tttt) cc_final: 0.6609 (mmmt) REVERT: A 265 ARG cc_start: 0.7821 (ptt180) cc_final: 0.7595 (ppt-90) REVERT: A 299 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: A 314 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: A 356 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7170 (mtm110) REVERT: A 386 MET cc_start: 0.8997 (ttm) cc_final: 0.8723 (ttp) REVERT: N 3 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: N 5 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7149 (tm-30) REVERT: N 87 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7905 (mtmt) REVERT: N 110 VAL cc_start: 0.9014 (t) cc_final: 0.8705 (m) outliers start: 33 outliers final: 22 residues processed: 150 average time/residue: 1.2660 time to fit residues: 202.0548 Evaluate side-chains 150 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.0870 chunk 90 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.0070 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127134 restraints weight = 9730.990| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.88 r_work: 0.3273 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8670 Z= 0.102 Angle : 0.484 9.080 11747 Z= 0.256 Chirality : 0.039 0.132 1330 Planarity : 0.004 0.063 1447 Dihedral : 5.657 59.427 1608 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.02 % Allowed : 21.39 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1021 helix: 2.78 (0.24), residues: 432 sheet: 0.04 (0.32), residues: 218 loop : -0.17 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 362 PHE 0.015 0.001 PHE R 288 TYR 0.011 0.001 TYR N 95 ARG 0.015 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 462) hydrogen bonds : angle 4.52431 ( 1347) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.70335 ( 6) covalent geometry : bond 0.00210 ( 8667) covalent geometry : angle 0.48391 (11741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.894 Fit side-chains REVERT: R 50 ARG cc_start: 0.6512 (mmt90) cc_final: 0.5660 (tpm170) REVERT: R 57 LYS cc_start: 0.7259 (mttt) cc_final: 0.6901 (mtmm) REVERT: R 265 LYS cc_start: 0.7605 (tttt) cc_final: 0.7269 (tmtm) REVERT: A 17 LYS cc_start: 0.7377 (tttt) cc_final: 0.6533 (mmmt) REVERT: A 265 ARG cc_start: 0.7812 (ptt180) cc_final: 0.7609 (ppt-90) REVERT: A 299 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7898 (pt0) REVERT: A 314 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: A 386 MET cc_start: 0.8971 (ttm) cc_final: 0.8687 (ttp) REVERT: B 124 TYR cc_start: 0.8776 (m-80) cc_final: 0.8405 (m-80) REVERT: N 3 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: N 5 GLN cc_start: 0.7878 (mm-40) cc_final: 0.6959 (tm-30) REVERT: N 35 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8534 (p0) REVERT: N 87 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7829 (mtmt) REVERT: N 94 TYR cc_start: 0.8959 (m-80) cc_final: 0.8749 (m-80) REVERT: N 109 ASP cc_start: 0.7273 (m-30) cc_final: 0.7058 (m-30) REVERT: N 110 VAL cc_start: 0.8883 (t) cc_final: 0.8662 (m) outliers start: 27 outliers final: 18 residues processed: 163 average time/residue: 1.1724 time to fit residues: 203.9519 Evaluate side-chains 149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 0.0770 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.152959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118855 restraints weight = 9887.452| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.97 r_work: 0.3190 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8670 Z= 0.127 Angle : 0.508 8.601 11747 Z= 0.266 Chirality : 0.040 0.160 1330 Planarity : 0.004 0.038 1447 Dihedral : 5.715 58.301 1608 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.58 % Allowed : 22.51 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1021 helix: 2.63 (0.24), residues: 438 sheet: -0.05 (0.31), residues: 219 loop : -0.15 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.005 0.001 HIS A 362 PHE 0.016 0.001 PHE R 288 TYR 0.009 0.001 TYR R 194 ARG 0.009 0.000 ARG R 226 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 462) hydrogen bonds : angle 4.58993 ( 1347) SS BOND : bond 0.00120 ( 3) SS BOND : angle 1.03677 ( 6) covalent geometry : bond 0.00277 ( 8667) covalent geometry : angle 0.50765 (11741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7152.76 seconds wall clock time: 122 minutes 33.72 seconds (7353.72 seconds total)